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NCBI C++ ToolKit: src/objtools/blast/blastdb_format/seq_writer.cpp Source File

: m_Out(

), m_FmtSpec(format_spec), m_BlastDb(blastdb),

m_DataExtractor(blastdb,

(

.m_FiltAlgoId >= 0 ||

.m_FmtAlgoId >= 0) {

(

.m_FiltAlgoId >= 0)

algo_ids.push_back(

.m_FiltAlgoId);

(

.m_FmtAlgoId >= 0)

algo_ids.push_back(

.m_FmtAlgoId);

vector<int> invalid_algo_ids =

( !invalid_algo_ids.empty()) {

);

);

os <<

<< *fmt <<

;

vector<string> data2write;

(*desc)->GetTitle();

kTarget(

);

kCtrlA =

(1,

) +

(

);

(

.IsGi() ||

.IsPrf() ||

.IsPir()) {

retval =

.AsFastaString();

retval =

.GetSeqIdString(

);

long_seqids =

;

long_seqids = (

.

(

,

) ==

);

(bioseq.

()) {

lcl_tmp =

->AsFastaString();

lcl_tmp = lcl_tmp.erase(0,4);

(long_seqids) {

(

.m_UseCtrlA) {

fasta.

(*bioseq, 0,

);

separator =

.m_UseCtrlA ?

:

;

>

SIZE_TYPE operator() (SIZE_TYPE a, const string& b) const {

CSeqFormatter::x_Replacer(const vector<string>& data2write) const

SIZE_TYPE data2write_size = accumulate(data2write.begin(), data2write.end(),

retval.reserve(m_FmtSpec.size() + data2write_size -

(m_ReplTypes.size() * 2));

SIZE_TYPE fmt_idx = 0;

for (SIZE_TYPE i = 0, kSize = m_ReplOffsets.size(); i < kSize; i++) {

retval.append(&m_FmtSpec[fmt_idx], &m_FmtSpec[m_ReplOffsets[i]]);

retval.append(data2write[i]);

fmt_idx = m_ReplOffsets[i] + 2;

if (fmt_idx <= m_FmtSpec.size()) {

retval.append(&m_FmtSpec[fmt_idx], &m_FmtSpec[m_FmtSpec.size()]);

void CSeqFormatter::SetConfig(TSeqRange range, objects::ENa_strand strand,

m_DataExtractor.SetConfig(range, strand, filt_algo_id);

Definition of a customizable sequence writer interface.

Encapsulates identifier to retrieve data from a BLAST database.

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

Defines invalid user input exceptions.

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

vector< int > ValidateMaskAlgorithms(const vector< int > &algorithm_ids)

Validates the algorithm IDs passed to this function, returning a vector of those algorithm IDs not pr...

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

void Write(CBlastDBSeqId &id)

Write the sequence data associated with the requested ID in the format specified in the constructor.

bool x_RequireData() const

Specifies whether or not data (e.g., Bioseq) is required.

CSeqFormatter(const string &fmt_spec, CSeqDB &blastdb, CNcbiOstream &out, CSeqFormatterConfig config=CSeqFormatterConfig())

Constructor.

vector< char > m_ReplTypes

Vector of convertor objects.

string x_Replacer(const vector< string > &data2write) const

Replace format specifiers for the data contained in data2write.

CNcbiOstream & m_Out

Stream to write output.

CBlastDBExtractor m_DataExtractor

Data extractor.

void DumpAll(CSeqDB &blastdb, CSeqFormatterConfig config=CSeqFormatterConfig())

Full database FASTA dump This is an optimized version that does not support range and mask retrieval.

void x_Builder(vector< string > &data2write)

Build data for write.

string m_FmtSpec

The output format specification.

vector< SIZE_TYPE > m_ReplOffsets

Vector of offsets where the replacements will take place.

CSeqDB & m_BlastDb

The BLAST database from which to extract data.

bool m_Fasta

Fasta output?

std::ofstream out("events_result.xml")

main entry point for tests

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

void SetWidth(TSeqPos width)

virtual void WriteSequence(const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly)

void SetAllFlags(TFlags flags)

@ fNoExpensiveOps

don't try too hard to find titles

@ fKeepGTSigns

don't convert '>' to '_' in title

@ fEnableGI

Use this flag to enable GI output in the defline.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

const TDb & GetDb(void) const

Get the Db member data.

bool IsGeneral(void) const

Check if variant General is selected.

bool IsLocal(void) const

Check if variant Local is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

list< CRef< CSeqdesc > > Tdata

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ e_Title

a title for this sequence

static void s_ReplaceCtrlAsInTitle(CRef< CBioseq > bioseq)

string GetBareId(const CSeq_id &id)

static string s_GetTitle(CConstRef< CBioseq > bioseq)

Configuration object for CSeqFormatter.

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